Variant report

Variant	rs66688634
Chromosome Location	chr7:150053806-150053807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150019092..150022415-chr7:150049163..150053845,5	K562	blood:
2	chr7:150018896..150021417-chr7:150052891..150055255,2	MCF-7	breast:
3	chr7:150053678..150054204-chr7:150075015..150075784,3	MCF-7	breast:
4	chr7:150025962..150028833-chr7:150053368..150055089,2	K562	blood:
5	chr7:150053181..150054101-chr7:150117910..150119216,10	MCF-7	breast:
6	chr7:150053210..150054184-chr7:150117715..150118824,10	K562	blood:
7	chr7:150019173..150023075-chr7:150052530..150058157,7	K562	blood:

Variant related genes	Relation type
ENSG00000188707	Chromatin interaction
ENSG00000127399	Chromatin interaction
ENSG00000106526	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10248490	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10259796	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10282458	0.94[ASN][1000 genomes]
rs10952252	0.94[ASN][1000 genomes]
rs1132261	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11767409	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11768108	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12703061	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13223702	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13238964	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13307276	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17173681	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17173682	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17173702	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17173703	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2098053	0.88[ASN][1000 genomes]
rs28432021	0.94[ASN][1000 genomes]
rs28439010	0.94[ASN][1000 genomes]
rs34311995	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34489187	0.93[ASN][1000 genomes]
rs34495356	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34728606	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35435439	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35635199	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35840727	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36035506	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36069544	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3735167	0.83[ASN][1000 genomes]
rs68107602	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6964110	0.87[ASN][1000 genomes]
rs71537957	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73170192	0.86[ASN][1000 genomes]
rs7800196	0.83[EUR][1000 genomes]
rs883138	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv889453	chr7:150009838-150104410	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv889454	chr7:150009838-150115183	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv889455	chr7:150013393-150104410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv889456	chr7:150013393-150115183	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv889457	chr7:150020295-150104410	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
11	nsv889458	chr7:150020295-150115183	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv521407	chr7:150020295-150118590	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv465211	chr7:150035526-150104410	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
14	nsv608991	chr7:150035526-150104410	Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
15	nsv889459	chr7:150041610-150071464	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv608992	chr7:150045910-150115183	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs66688634	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs66688634	REPIN1	cis	Muscle Skeletal	GTEx
rs66688634	LRRC61	cis	Thyroid	GTEx
rs66688634	LRRC61	cis	Muscle Skeletal	GTEx
rs66688634	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs66688634	LRRC61	cis	Esophagus Mucosa	GTEx
rs66688634	LRRC61	cis	Nerve Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150039200-150065000	Weak transcription	Right Atrium	heart
2	chr7:150044000-150058000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:150049600-150054400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:150049800-150054600	Weak transcription	Placenta	Placenta
5	chr7:150051200-150056600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:150051400-150054400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:150052000-150061000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr7:150052200-150056600	Enhancers	Primary hematopoietic stem cells	blood
9	chr7:150052400-150054400	Enhancers	GM12878-XiMat	blood
10	chr7:150052400-150054800	Enhancers	K562	blood
11	chr7:150052400-150055200	Enhancers	Adipose Nuclei	Adipose
12	chr7:150052600-150054600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr7:150052600-150054800	Enhancers	Liver	Liver
14	chr7:150053000-150054400	Weak transcription	Colonic Mucosa	Colon
15	chr7:150053000-150054600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr7:150053000-150056400	Weak transcription	Fetal Kidney	kidney
17	chr7:150053000-150058000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:150053000-150058400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:150053200-150054000	Weak transcription	Thymus	Thymus
20	chr7:150053200-150054400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:150053200-150054400	Weak transcription	A549	lung
22	chr7:150053200-150055200	Enhancers	Primary B cells from peripheral blood	blood
23	chr7:150053200-150065000	Enhancers	Fetal Thymus	thymus
24	chr7:150053400-150054400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr7:150053400-150054400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr7:150053400-150054400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr7:150053400-150056400	Enhancers	Primary T cells from cord blood	blood
28	chr7:150053400-150056400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:150053400-150056600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr7:150053600-150054000	Enhancers	Brain Anterior Caudate	brain
31	chr7:150053600-150054200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:150053600-150054400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:150053600-150054400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr7:150053600-150054400	Enhancers	HepG2	liver
35	chr7:150053600-150055200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr7:150053600-150055200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:150053800-150054000	Enhancers	Fetal Intestine Large	intestine
38	chr7:150053800-150054000	Enhancers	Fetal Intestine Small	intestine
39	chr7:150053800-150054200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr7:150053800-150054200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:150053800-150054400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr7:150053800-150054400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr7:150053800-150054400	Enhancers	HSMM	muscle
44	chr7:150053800-150054800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr7:150053800-150055200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:150053800-150055200	Enhancers	Duodenum Mucosa	Duodenum
47	chr7:150053800-150055200	Flanking Active TSS	Dnd41	blood
48	chr7:150053800-150055400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr7:150053800-150055400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr7:150053800-150055400	Enhancers	HSMMtube	muscle

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